Hello. Sorry for contributing not with the technical questions/solutions, but with "user would like to....".
In your expert opinion how difficult would be to implement the following functionality to Jmol (polymers=proteins again, my nemesis): INPUT: a. pdb file of a protein (no indexing issues, ideal case) of N residues (amino acids). b. NxN matrix relating somehow all pairs of residues i<>j in the N-mer. This is flat text file (any format, user is responsible for it) GOAL: c. Load the protein to Jmol as usual. d. Tell Jmol that the NxN file related to the protein should be loaded to say internal matrix M (Menu item) e. Create a window WM (WM is connected to the protein plot in Jmol window see below) with contour plot of the profile defined by M and allow user to vary the z-axis threshold (goal: If maxima of M-defined profile is what I need to see, it would be nice to have a slider with Zmax-Zmin interval, that I can drag and the contours would start from the z-threshold thus defined..optimally, one can move both lower and upper threshold to see a "slice"). f. If I (left-?)-click on the feature in WM, the i and j coordinates (in real units, i.e. in the indices of monomers i and j, corresponding to the selected element of M) are read, and transferred to the "select i,j" command issued for the protein. At the same time, the selection should be somehow visualized, either by immediate (automatic) coloring of the residues i and j or by rendering them in stick or CPK. Toggle by right-click this would de-select the residues in mol. plot and restore previous rendering of them. g. If I drag a rectangle in WM window, the boundaries of that rectangle would be identified as i and j and transferred to protein structure plot by "select i-j" with the similar visualization (color, residue rendering). Somehow then I should be able to de-select the region again from the WM window (say by left click inside the rectangle?). Any one knows about a viewer with such a functionality? VM had something like that but not very flexible and handy. What I am using to emulate this functionality is sort of "off-line" combination of a script in R which I run parallel to Jmol. R reads the matrix, generates the plot, allows me to do the z-clipping and reads-out the features in terms of residue i, residue j pairs with printing them in R-text window as "select i,j" or "select i-j". I then copy/paste those to Jmol/Rasmol command line window + some additional clicking. If this sounds doable, where to start? Not much experience with Jmol code, so most probably I need to learn a lot first.... Thanks, PP Dr. Petr Pancoska Department of Pathology SUNY Stony Brook, NY 11794 phone: (631)-444-3030 ****************************************************************************** This e- mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ****************************************************************************** ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
